Merge pull request #1257 from RosettaCommons/tlinsky/store_residue_subset
Add StoreResidueSubset mover/StoredResidueSubset res selector
Store_residue_subset is a new integration test
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Merge pull request #1251 from RosettaCommons/tlinsky/add_csts_to_current_conformation_mover
Fix bug in setting up TaskSelector in AddConstraintsToCurrentConformationMover
Integration test change expected in task_selector since the input changed slightly.
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Merge pull request #1255 from RosettaCommons/roccomoretti/option_spellcheck
Add "spell check" for options.
Add diagnostic output to suggest possible alternatives when a commandline option is not recognized due to:
* Wrong namespace (-out:file:pdb vs. -out:pdb)
* Wrong underscores (-out:file:scoreonly vs. -out:file:score_only)
* Wrong case (-flip_hnq vs. -flip_HNQ)
* Simple typos (-in:file:tagsfile vs. -in:file:tagfile; -out:perfex vs. -out:prefix)
(Note the typo detection is rather basic, and prone to over-suggesting - don't expect miracles.)
This is separate from (and subordinate to) the existing detection of ambiguous options.
This code should only trigger when Rosetta would have exited with an unrecognized option.
If you accidentally use the wrong option, it's not going to help.
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Adding Intel libraries needed for linking icc build to basic.settings settings for icc. Merging without testing, since this shouldn't affect any test-server build.
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Merge pull request #1254 from RosettaCommons/JWLabonte/sugars/branching
Post-ChemicalXRW: Fix bug introduced during purging of LINK records
This merge fixes a bug introduced during the ChemicalXRW (by Andy :p) that broke the way branches were assigned from .pdb files involving sugars and adds a unit test so that this does not happen again. :)
This also adds another sugar .params file, which will permit core fucosylated N-glycans in PDB format to be loaded. (Before, they could only be loaded with Rosetta-format HETNAM records, and I failed to notice that.)
All unit tests pass. Minor integration test changes do to changes in input files and help output.
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Merge pull request #1205 from RosettaCommons/everyday847/fix_chi_bug
Miscellaneous metalloprotein fixes.
- auto_setup_metals now is properly behaved with the new metapatching system
- auto_setup_metals now works with cartesian minimization
Integration tests will fail due to either:
a) changing the level of some tracer output in ResidueProperties
b) adding a new score term
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Merge pull request #1240 from RosettaCommons/vmullig/peppredict_setting
Fixing a minor bug in the simple_cycpep_predict app
When the user set certain residues to have certain dihedral values, the wrong residue was sometimes being set when the pose was circularly permuted. This affected the efficiency of sampling, but would not invalidate the scientific results (so this bugfix need not be pushed to BOINC immediately, @davidekim -- it can wait for whenever the next BOINC update happens).
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Merge pull request #1242 from RosettaCommons/vmullig/fix_splice_test
Attempting to fix the splice_out_L1_L2_longer integration test
Changing the random seed for the splice_out_L1_L2_longer integration test. This test's success is highly dependent on the seed value, and for many seeds, it fails to find a solution that passes filters. The switch to lbfgs minimization caused enough of a trajectory change that this test started failing.
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